Different scaling of linear models and deep learning in UKBiobank brain images versus machine-learning datasets

• Published in: Nature communications 2020-08, Vol.11 (1), p.4238-15, Article 4238
• Main Authors: Schulz, Marc-Andre, Yeo, B. T. Thomas, Vogelstein, Joshua T., Mourao-Miranada, Janaina, Kather, Jakob N., Kording, Konrad, Richards, Blake, Bzdok, Danilo
• Format: Article
• Language: English
• Subjects: 49; 59/36; 59/57; 631/378/116/2394; 706/648/697/129/2043; Algorithms; Biological Specimen Banks; Brain; Brain - diagnostic imaging; Datasets; Deep Learning; Depth profiling; Humanities and Social Sciences; Humans; Kernels; Learning algorithms; Linear Models; Machine Learning; multidisciplinary; Neuroimaging - methods; Phenotype; Phenotypes; Predictions; Sample Size; Science; Science (multidisciplinary); Structure-function relationships; United Kingdom
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-18037-z

Recently, deep learning has unlocked unprecedented success in various domains, especially using images, text, and speech. However, deep learning is only beneficial if the data have nonlinear relationships and if they are exploitable at available sample sizes. We systematically profiled the performance of deep, kernel, and linear models as a function of sample size on UKBiobank brain images against established machine learning references. On MNIST and Zalando Fashion, prediction accuracy consistently improves when escalating from linear models to shallow-nonlinear models, and further improves with deep-nonlinear models. In contrast, using structural or functional brain scans, simple linear models perform on par with more complex, highly parameterized models in age/sex prediction across increasing sample sizes. In sum, linear models keep improving as the sample size approaches ~10,000 subjects. Yet, nonlinearities for predicting common phenotypes from typical brain scans remain largely inaccessible to the examined kernel and deep learning methods. Schulz et al . systematically benchmark performance scaling with increasingly sophisticated prediction algorithms and with increasing sample size in reference machine-learning and biomedical datasets. Complicated nonlinear intervariable relationships remain largely inaccessible for predicting key phenotypes from typical brain scans.